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- PDB-9q65: Human prolyl endopeptidase (PREP) - complex with KT-2-75 -

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Basic information

Entry
Database: PDB / ID: 9q65
TitleHuman prolyl endopeptidase (PREP) - complex with KT-2-75
ComponentsProlyl endopeptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / inhibitor-bound / peptide cleavage / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


prolyl oligopeptidase / oligopeptidase activity / angiotensin maturation / metallocarboxypeptidase activity / serine-type peptidase activity / serine-type endopeptidase activity / proteolysis / extracellular region / nucleus / membrane ...prolyl oligopeptidase / oligopeptidase activity / angiotensin maturation / metallocarboxypeptidase activity / serine-type peptidase activity / serine-type endopeptidase activity / proteolysis / extracellular region / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / Prolyl endopeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsFucci, I.J. / Thakur, K. / Pandian, J. / Yoo, E. / Monteiro, D.C.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J.Med.Chem. / Year: 2026
Title: Structure-Guided Optimization of 4-Chloro-Pyrazolopyridine Analogs for Covalent PREP Inhibition.
Authors: Thakur, K. / Fucci, I. / Pandian, J. / Suazo, K.F. / Monteiro, D.C.F. / Yoo, E.
History
DepositionAug 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Prolyl endopeptidase
D: Prolyl endopeptidase
F: Prolyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,07722
Polymers242,5543
Non-polymers2,52319
Water7,494416
1
B: Prolyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,17612
Polymers80,8511
Non-polymers1,32511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Prolyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5366
Polymers80,8511
Non-polymers6845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: Prolyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3654
Polymers80,8511
Non-polymers5143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.522, 65.986, 159.33
Angle α, β, γ (deg.)90, 100.473, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules BDF

#1: Protein Prolyl endopeptidase / PE / Post-proline cleaving enzyme


Mass: 80851.367 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PREP, PEP / Production host: Escherichia coli (E. coli) / References: UniProt: P48147, prolyl oligopeptidase

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Non-polymers , 6 types, 435 molecules

#2: Chemical ChemComp-A1CQU / 4-chloro-1,3-dimethyl-N-[3-oxo-3-(pyrrolidin-1-yl)propyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide


Mass: 349.815 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H20ClN5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CNS
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979338 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 1.89→34.6 Å / Num. obs: 121039 / % possible obs: 91.7 % / Redundancy: 7.1 % / Biso Wilson estimate: 20.6 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.37 / Rpim(I) all: 0.149 / Rrim(I) all: 0.399 / Net I/σ(I): 4.6
Reflection shellResolution: 1.89→2.08 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.447 / Num. unique obs: 6052 / CC1/2: 0.22 / Rpim(I) all: 0.576 / Rrim(I) all: 1.558 / % possible all: 58.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.100)refinement
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→34.6 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.842 / SU B: 7.489 / SU ML: 0.113 / Cross valid method: FREE R-VALUE / ESU R: 0.063 / ESU R Free: 0.053
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2954 6051 4.999 %
Rwork0.2184 114988 -
all0.222 --
obs-121039 69.672 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.884 Å2
Baniso -1Baniso -2Baniso -3
1-0.077 Å20 Å22.485 Å2
2---2.125 Å20 Å2
3---2.048 Å2
Refinement stepCycle: LAST / Resolution: 1.89→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16992 0 161 416 17569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01217630
X-RAY DIFFRACTIONr_bond_other_d0.0010.01616107
X-RAY DIFFRACTIONr_angle_refined_deg2.0581.81823888
X-RAY DIFFRACTIONr_angle_other_deg0.6711.76337227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2152123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.5976.93593
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg6.69353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.878102905
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.84110852
X-RAY DIFFRACTIONr_chiral_restr0.0920.22516
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0220694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024110
X-RAY DIFFRACTIONr_nbd_refined0.230.23603
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.216111
X-RAY DIFFRACTIONr_nbtor_refined0.1930.28544
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.29411
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2688
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0670.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2470.242
X-RAY DIFFRACTIONr_nbd_other0.2790.2130
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2660.214
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1330.21
X-RAY DIFFRACTIONr_mcbond_it1.1451.4328489
X-RAY DIFFRACTIONr_mcbond_other1.1441.4328483
X-RAY DIFFRACTIONr_mcangle_it1.6142.57210603
X-RAY DIFFRACTIONr_mcangle_other1.6142.57210604
X-RAY DIFFRACTIONr_scbond_it1.1631.4949141
X-RAY DIFFRACTIONr_scbond_other1.1631.4949142
X-RAY DIFFRACTIONr_scangle_it1.6532.71613283
X-RAY DIFFRACTIONr_scangle_other1.6532.71613284
X-RAY DIFFRACTIONr_lrange_it2.24414.19719702
X-RAY DIFFRACTIONr_lrange_other2.24414.19719703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.9360.25960.301145X-RAY DIFFRACTION1.1838
1.936-1.9890.407580.2641128X-RAY DIFFRACTION9.5208
1.989-2.0460.3361300.2522605X-RAY DIFFRACTION22.6539
2.046-2.1090.3771940.2523928X-RAY DIFFRACTION34.9144
2.109-2.1780.3662950.2555244X-RAY DIFFRACTION48.6945
2.178-2.2550.3623630.2546754X-RAY DIFFRACTION64.4948
2.255-2.340.3624370.2498944X-RAY DIFFRACTION87.9112
2.34-2.4360.3394950.2479241X-RAY DIFFRACTION94.5059
2.436-2.5440.334690.2499242X-RAY DIFFRACTION98.6189
2.544-2.6680.3384810.2428909X-RAY DIFFRACTION99.9468
2.668-2.8120.3344270.248544X-RAY DIFFRACTION100
2.812-2.9830.3044280.2388085X-RAY DIFFRACTION100
2.983-3.1890.3084070.2277626X-RAY DIFFRACTION100
3.189-3.4440.2763760.2087069X-RAY DIFFRACTION100
3.444-3.7720.2573700.196492X-RAY DIFFRACTION99.9854
3.772-4.2170.2583070.1725919X-RAY DIFFRACTION100
4.217-4.8690.2292840.1665210X-RAY DIFFRACTION99.9818
4.869-5.9620.2342510.1894465X-RAY DIFFRACTION100
5.962-8.4260.2891680.2143488X-RAY DIFFRACTION100
8.426-34.60.2271050.2291950X-RAY DIFFRACTION98.2783
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.23910.0586-0.01410.2211-0.04880.18690.0081-0.02370.00120.024-0.0106-0.0181-0.01380.01370.00260.0033-0.0007-0.00230.0089-0.00180.0024-2.25550.653555.2317
20.278-0.0258-0.05270.2188-0.03330.1798-0.00110.0108-0.0080.0131-0.004-0.02140.0270.01920.00520.01740.0091-0.00930.0306-0.00730.008526.5839-0.1728105.8235
30.15540.0421-0.06090.1795-0.0620.28210.01360.0023-0.00090.0012-0.0117-0.01020.00450.0155-0.00190.0330.0081-0.01350.0354-0.00830.007550.9771-4.4632158.6007
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLBp5 - 710
2X-RAY DIFFRACTION2ALLDp5 - 710
3X-RAY DIFFRACTION3ALLFp5 - 710

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